Plastid and mitochondria
What is difference between plastid, chloroplast and mitochondira?


Plastid is a general term for an organelle which consists of Chloroplasts, Chromoplasts, Leukoplasts/Amyloplasts and Apicoplasts.

Chloroplasts (Chloro = green) are involved in photosynthesis; they express Chlorophylls and have the thylakoid structures which are involved in the electron transport chain that results in ATP formation during the light reactions of photosynthesis. As it is obvious chloroplasts are found in the green parts of the plants such as leaves. Chloroplasts also have the enzymes of biosynthetic pathways involved in carbon fixation. 

Chromoplasts (Chromo = colored) express more of other pigments and less of chlorophyll. Neither do they have thylakoid structures. Therefore they are not involved in photosynthesis. When fruits ripen, the chloroplasts differentiate to chromoplasts. Flowers also contain a lot of chromoplasts.

Leukoplasts (Leuko = white) do not have any pigments and usually carry out biosynthetic processes. When they store starch they are called amyloplasts. 

Apicoplasts are found in parasites like plasmodia (causes malaria) and are vital for their survival. The Apicoplast is involved in biosynthetic pathways but the precise importance of it remains unknown.

The mitochondrion is a very different organelle and has a different evolutionary origin. Mitochondria, like Chloroplasts, produce ATP from an electron transport chain but use chemical substrates (NADH, flavin etc) rather than light as a source of initial energy. Mitochondria are thought to be an outcome of an endosymbiosis between an ancestral eukaryotic cell and an $\alpha$-proteobacterium. Chloroplasts, on the other hand have descended from a Cyanobacterial endosymbiont. Therefore the structure of mitochondria is very different from that of chloroplasts. 

Chromoplasts, leukoplasts, amyloplasts and apicoplasts have lost the photosynthetic ability. Similarly, there are variants of mitochondria which use different electron acceptors (other than oxygen) and some are just incapable of ATP synthesis. 


  Are there any plant sequence database for each of them (plastid,
  chloroplast and mitochondira)?


Chloroplast genome database: {link}

I don't know of a separate plant mitochondrial database but you can see this resource called MitBASE.

NCBI also has the organellar DNA sequences. 


  Can we separate as chloroplast, mitochondria, platid sequence from
  whole genome assembly?


Usually the organellar genomes will assemble as separate contigs when you sequence from the whole cell DNA prep. By homology it is possible to say if the contig is a mitochondrial or chloroplast DNA. But the best way would be to experimentally isolate the organelles and sequence their DNA.